Please note that this page contains numerous links and download buttons, which may take a few minutes to load completely.

Course Papers

  • Hierarchical Models Weinberger and Warren et al. 2020 (view paper)
  • Serotype Replacement Weinberger and Warren et al. 2018 (view paper)
  • Correlates of Nonrandom Patterns of Serotype Switching in Pneumococcus Joshi and Al-Mamun et al. 2020 (view paper)
  • 2022 Annual Epidemiological Report for Invasive Pneumococcal Disease (IPD) (view paper)

Lecture Slides

Codespaces

Weekly Modules

Please download the codespaces provided for each weekly module release. Note that you may need to adjust the filepath for some references inside the code. It is recommended that you use the starter codespace package, which includes the following:

  • An Rproj file to set your root directory.
  • An renv lockfile.
  • A suggested .gitignore.
  • A README.md file with directions for using the codespace and guidelines for adding the code to your own GitHub remote repository.

Subsequent weekly releases should be placed inside your root project directory. For instance, if you are using the directory “~/bdsy-phm-individual”, place the weekly releases within that directory.

Project Datasets and Materials

  • Complete Global Pneumococcal Sequencing Project (GPS) Data Viewer and Download (link to page)

  • Peru Epidemiological surveillance of Acute Respiratory Infections (ARI) Data Page (link to page)

Templates

Tips and Advice

Research Like a Pro

It is vital that you keep track of and disclose all the references you use to support your research. There are many tools available to help you with this, so discuss with your team and decide on a preferred method for reference tracking.

In my research, I use Mendeley, which comes with a Web Importer plug-in that makes it easy to compile different types of references. It conveniently formats these entries to various styles, including LaTeX and BibTeX.

Back to top